Nitrogen run off into Long Island Sound (LIS) and resulting eutrophication-driven hypoxia can be effectively mitigated with year round seaweed aquaculture. Geographic information systems (GIS) offers an invaluable tool for optimizing site selection. To maximize on an annual basis both nutrient removal and crop biomass, two species (sugar kelp Saccharina latissima and the red seaweed Gracilaria tikvaiae) were examined in this model. Unrestricted farmable areas of LIS were first identified. Water column data for these areas was then analyzed including; nitrogen, phosphorus, and chlorophyll-a concentrations, as well as temperature, salinity, and dissolved oxygen. Using GIS, seasonal and monthly variations in these water quality parameters allow planners to identify optimum planting times and areas as well as determine site specific crop biomass and nutrient removal capacity.